From the commentary: "That, the Galaga joke was added after the fact because that extra just looked shifty. So we actually hadn't intended that on the day we saw the second unit footage of that guy turning back to his console we thought let's just see what happens."

I thought the line was improvised by Downey, and then the footage was added even latered because the extra looked so shifty...

Not that it really matters much, considering how weird it is to consider that scene 'important foreshadowing' in the first place, despite how many other far more direct references are made early in the movie to an alien army. (Just because they came from above, that makes the Galaga important? Where else would an alien army ever come from?)